ENST00000425939.1:n.440+3045T>A

Variant names:

• chr20-16727464-A-T
• rs3787509
• ENST00000425939.1:n.440+3045T>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000425939.1(ENSG00000228809):​n.440+3045T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.751 in 152,154 control chromosomes in the GnomAD database, including 43,564 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.75 (43564 hom., cov: 32)
• Consequence: ENSG00000228809 ENST00000425939.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• Publications: 6 publications found

Genes affected

ENSG00000228809 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228809	ENST00000425939.1	n.440+3045T>A		intron_variant	Intron 1 of 3	5
ENSG00000228809	ENST00000613736.2	n.452+1965T>A		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114196 AN: 152036 Hom.: 43504 Cov.: 32

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.727

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.751 AC: 114316 AN: 152154 Hom.: 43564 Cov.: 32 AF XY: 0.751 AC XY: 55854 AN XY: 74360

African (AFR) AF: 0.891 AC: 37021 AN: 41544

American (AMR) AF: 0.674 AC: 10305 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2346 AN: 3470

East Asian (EAS) AF: 0.658 AC: 3400 AN: 5168

South Asian (SAS) AF: 0.783 AC: 3778 AN: 4822

European-Finnish (FIN) AF: 0.698 AC: 7368 AN: 10560

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.704 AC: 47830 AN: 67984

Other (OTH) AF: 0.726 AC: 1536 AN: 2116

Alfa AF: 0.734 Hom.: 5132

Bravo AF: 0.754

Asia WGS AF: 0.700 AC: 2432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	9.2
DANN	Benign	0.74
PhyloP100		0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3787509; hg19: chr20-16708109;